Comparison between the types for the ages and genders¶
Questions
- What are the differences between the type for the different combinations of ages and genders?
- Do we observe the same changes as globally?
Allowing multi-threading with up to 4 threads. [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..."
Data¶
Stats¶
| Wald padj < 0.05 | LFC > 0 (Wald padj < 0.05) | LFC < 0 (Wald padj < 0.05) | |
|---|---|---|---|
| GF VS SPF (F, 8w) | 392 | 192 | 200 |
| GF VS SPF (M, 8w) | 161 | 76 | 85 |
| GF VS SPF (F, 52w) | 738 | 316 | 422 |
| GF VS SPF (M, 52w) | 393 | 145 | 248 |
| GF VS SPF (F, 104w) | 2038 | 846 | 1192 |
| GF VS SPF (M, 104w) | 2172 | 898 | 1274 |
Differentially expressed genes¶
GF VS SPF (F, 8w) GF VS SPF (M, 8w) GF VS SPF (F, 52w) GF VS SPF (M, 52w)
0.5790816 0.6832298 0.4363144 0.6030534
GF VS SPF (F, 104w) GF VS SPF (M, 104w)
0.5662414 0.5382136
Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in stack.default(getgo(rownames(l$deg), "mm10", "geneSymbol")): “non-vector elements will be ignored”Warning message in stack.default(getgo(rownames(as.data.frame(l$deg)), "mm10", "geneSymbol", : “non-vector elements will be ignored”
Warning message: “Removed 14812 rows containing non-finite values (stat_density).”
Comparison of the numbers per ages¶
Differentially expressed genes
DEG into gene co-expression network¶
- White: up-regulated
- Black: down-regulated
| GF vs SPF | 8w | 52w | 104w |
|---|---|---|---|
| F | |||
| M |
GO analysis¶
Biological process¶
Dot-plot with the 20 most significant p-values for the different comparison
Using term, id as id variables Using term, id as id variables
Network based on description similarity
| GF vs SPF | 8w | 52w | 104w |
|---|---|---|---|
| F | |||
| M |
GF VS SPF (F, 8w)
<!DOCTYPE html>
GF VS SPF (M, 8w)
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GF VS SPF (F, 52w)
<!DOCTYPE html>
GF VS SPF (M, 52w)
<!DOCTYPE html>
GF VS SPF (F, 104w)
<!DOCTYPE html>
GF VS SPF (M, 104w)
<!DOCTYPE html>
Cellular components¶
Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)
Using term, id as id variables Using term, id as id variables
Molecular functions¶
Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)
Using term, id as id variables Using term, id as id variables
KEGG pathways¶
[1] "Note: 5 of 3451 unique input IDs unmapped." [1] "Note: 5 of 3451 unique input IDs unmapped."
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Pathway graphs available at ../results/dge/type-effect/type_gender_age/over_repr_kegg/
[1] "Note: 5 of 3451 unique input IDs unmapped."
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[1] "Note: 5 of 3451 unique input IDs unmapped." [1] "Note: 5 of 3451 unique input IDs unmapped." [1] "Note: 5 of 3451 unique input IDs unmapped."
Pathway graphs available at ../results/dge/type-effect/type_gender_age/under_repr_kegg/
Comparison with Erny results¶
Protocol: 2 months old female mices (GF vs SPF)
Raw comparison of the results¶
| Symbols | Genes | fold.d.h | GF_1 | GF_2 | GF_3 | GF_4 | GF_5 | GF_7 | GF_8 | SPF_1 | SPF_2 | SPF_3 | SPF_4 | SPF_6 | SPF_7 | SPF_8 | t.test |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ddit4 | NM_029083 | 3.488386 | 232 | 420 | 140 | 116 | 1027 | 785 | 501 | 40 | 21 | 22 | 13 | 73 | 70 | 48 | 0.007198903 |
| Iqgap1 | NM_016721 | 2.545650 | 24 | 44 | 10 | 16 | 20 | 17 | 50 | 4 | 14 | 2 | 3 | 1 | 6 | 1 | 0.003764139 |
| Tsc22d3 | NM_001077364 | 2.416164 | 47 | 107 | 44 | 53 | 257 | 214 | 132 | 23 | 17 | 23 | 20 | 39 | 16 | 22 | 0.009737505 |
| Rab3d | NM_031874 | 2.369234 | 7 | 14 | 5 | 10 | 2 | 7 | 17 | 1 | 1 | 1 | 1 | 3 | 1 | 4 | 0.004171454 |
| Gnaz | NM_010311 | 2.280108 | 1 | 1 | 5 | 5 | 9 | 9 | 4 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.009123198 |
| Agpat4 | NM_026644 | 1.984893 | 5 | 21 | 21 | 10 | 15 | 10 | 13 | 4 | 7 | 1 | 1 | 5 | 5 | 1 | 0.001279054 |
- 1700037C18Rik
- -0.726653411890693
- 1700112E06Rik
- -3.64638532054075
- 1810011O10Rik
- 1.05252272836875
- Ccdc191
- -1.07325728126671
- 2610524H06Rik
- 1.32511199395419
- 6330407A03Rik
- -1.99177874144356
| erny | our | |
|---|---|---|
| Ddit4 | 3.4883860 | 3.6294025 |
| Tsc22d3 | 2.4161642 | 1.4193018 |
| Notch4 | 1.4226911 | 1.6315226 |
| Sult1a1 | 1.2561528 | 1.1617315 |
| Capg | 0.9126729 | 0.5168264 |
| Ucp2 | 0.9111967 | 0.5044607 |
| Gpr137b | 0.8032544 | 1.2266600 |
| Pnpla2 | 0.7100179 | 0.4259134 |
| Ogfrl1 | 0.6877922 | 0.6959325 |
| Arhgef6 | -1.0246621 | 0.4253851 |
| Gpr137b-ps | -1.1178365 | -3.0251734 |
| Upk1b | -1.1300605 | -0.6517569 |
| Cntrl | -1.3303078 | -0.9347969 |
| Apobec2 | -1.4288433 | -0.8472098 |
| Ly86 | -1.4389640 | -0.9562232 |
| Stard3nl | -1.4780473 | -0.4310033 |
| Fkbp7 | -1.6261852 | -0.3942576 |
| Malat1 | -1.7120031 | -1.1023659 |
| Mcur1 | -1.7424200 | -0.8593199 |
| Nos1ap | -1.8022360 | -0.8171791 |
| Zfp318 | -1.8961642 | -0.7895965 |
| Lrba | -2.0198996 | -0.6372855 |
| Far1 | -2.5766472 | 0.5588240 |
| Ero1lb | -3.2172307 | -1.3952799 |
Detailed comparison¶
- Checking the correlation between the counts of Erny and our counts
- Re-running a DGE analysis on the Erny's raw counts
Error in counts[, SPF_F_8w_samples]: object of type 'closure' is not subsettable Traceback: